gene expression. gene expression all cells in one organism have the same dna. but different cells...
TRANSCRIPT
![Page 1: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/1.jpg)
Gene Expression
![Page 2: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/2.jpg)
Gene expression
• All cells in one organism have the same DNA. But different cells have very different functions.
• In each cell at certain times only some genes are expressed.
• Which genes are expressed at which times?
![Page 3: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/3.jpg)
Cells
• muscle
• nerve
![Page 4: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/4.jpg)
Double-stranded DNA
![Page 5: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/5.jpg)
DNA Structure
![Page 6: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/6.jpg)
DNA matching
• Every A forms two weak hydrogen bonds with T.
• Every T forms two hydrogen bonds with A.
• Every C forms three weak hydrogen bonds with G.
• Every G forms three hydrogen bonds with C.
![Page 7: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/7.jpg)
RNA
• RNA is also a sequence of nucleotides.
• RNA means “ribonucleic acid”.
• DNA means “deoxyribonucleic acid”.
![Page 8: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/8.jpg)
Nucleotides
![Page 9: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/9.jpg)
RNA
![Page 10: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/10.jpg)
DNA Structure
![Page 11: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/11.jpg)
DNA vs RNA
• Both are strings of nucleotides.• DNA is usually double-stranded; RNA is
single-stranded.• RNA is usually much shorter than DNA.• RNA replaces each T by U (uracil).• DNA contains deoxyribose while RNA
contains ribose. This makes DNA more stable chemically than RNA.
![Page 12: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/12.jpg)
DNA and RNA
• DNA in your cells is in the nucleus; RNA can be anywhere in the cell.
• Proteins are made directly using RNA, not DNA.
![Page 13: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/13.jpg)
Central Dogma
• A protein-coding region of DNA is copied to messenger RNA (mRNA) by transcription.
• The mRNA leaves the nucleus and goes to a ribosome.
• The ribosome uses the mRNA to make a protein by translation.
![Page 14: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/14.jpg)
Central Dogma
![Page 15: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/15.jpg)
Translating codons• Ala/A GCT, GCC, GCA, GCG Leu/L TTA, TTG, CTT, CTC, CTA, CTG• Arg/R CGT, CGC, CGA, CGG, AGA, AGG Lys/K AAA, AAG• Asn/N AAT, AAC Met/M ATG• Asp/D GAT, GAC Phe/F TTT, TTC• Cys/C TGT, TGC Pro/P CCT, CCC, CCA, CCG• Gln/Q CAA, CAG Ser/S TCT, TCC, TCA, TCG, AGT, AGC• Glu/E GAA, GAG Thr/T ACT, ACC, ACA, ACG• Gly/G GGT, GGC, GGA, GGG Trp/W TGG• His/H CAT, CAC Tyr/Y TAT, TAC• Ile/I ATT, ATC, ATA Val/V GTT, GTC, GTA, GTG• START ATG STOP TAG, TGA, TAA
![Page 16: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/16.jpg)
Protein primary structure
![Page 17: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/17.jpg)
3D views of proteins
![Page 18: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/18.jpg)
DNA for beta hemoglobin
• ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAA
![Page 19: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/19.jpg)
Primary structure for beta hemoglobin
• MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
![Page 20: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/20.jpg)
Part of the two strands for beta hemoglobin
• ATGGTGCATCTGACTCCT…
• TACCACGTAGACTGAGGA…
• The top is the sense or template; the bottom is the antisense or coding strand.
![Page 21: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/21.jpg)
Transcription: Make mRNA
• ATGGTGCATCTGACTCCT… sense
• TACCACGTAGACTGAGGA… coding
• AUGGUGCAUCUGACUCCU… mRNA
![Page 22: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/22.jpg)
Structure of mRNA
![Page 23: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/23.jpg)
mRNA goes to a ribosome, outside the nucleus
• AUGGUGCAUCUGACUCCU… mRNA
![Page 24: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/24.jpg)
Eukaryotic cell
• (1) nucleolus• (2) nucleus• (3) ribosomes (little
dots)• (5) rough endoplasmic
reticulum (ER)• (9) mitochondria• (10) vacuole• (11) cytoplasm
![Page 25: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/25.jpg)
Ribosomes
• The ribosome functions as a factory to make proteins. It uses two kinds of input:
• (a) mRNA
• (b) tRNA
• It outputs a protein.
![Page 26: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/26.jpg)
Ribosome translates mRNA
• Ribosome (2) straddles mRNA (1)• It makes the protein (3).• It starts at AUG and ends at UAG
![Page 27: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/27.jpg)
Ribosome large subunit
![Page 28: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/28.jpg)
Transfer RNA (tRNA)
• Each tRNA molecule has on one side a conformation that binds to the specific codon and on the other side a conformation that binds to the corresponding amino acid.
![Page 29: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/29.jpg)
tRNA
• CCA tail in orange, Acceptor stem in purple, D arm in red, Anticodon arm in blue with Anticodon in black, T arm in green.
![Page 30: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/30.jpg)
tRNA carries the amino acid matched to the codon
• UAC … M tRNA will bind with the codon AUG in the mRNA.
• CAC … V tRNA will bind with the codon GUG in the mRNA.
![Page 31: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/31.jpg)
mRNA in a ribosome has the genetic information
• AUGGUGCAUCUGACUCCU…
• UAC … M tRNA will bind with the codon AUG.
• CAC … V tRNA will bind with the codon GUG.
![Page 32: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/32.jpg)
Translating codons• Ala/A GCT, GCC, GCA, GCG Leu/L TTA, TTG, CTT, CTC, CTA, CTG• Arg/R CGT, CGC, CGA, CGG, AGA, AGG Lys/K AAA, AAG• Asn/N AAT, AAC Met/M ATG• Asp/D GAT, GAC Phe/F TTT, TTC• Cys/C TGT, TGC Pro/P CCT, CCC, CCA, CCG• Gln/Q CAA, CAG Ser/S TCT, TCC, TCA, TCG, AGT, AGC• Glu/E GAA, GAG Thr/T ACT, ACC, ACA, ACG• Gly/G GGT, GGC, GGA, GGG Trp/W TGG• His/H CAT, CAC Tyr/Y TAT, TAC• Ile/I ATT, ATC, ATA Val/V GTT, GTC, GTA, GTG• START ATG STOP TAG, TGA, TAA
![Page 33: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/33.jpg)
mRNA goes to a ribosome
• AUGGUGCAUCUGACUCCU… mRNA
• UAC …. M tRNA• CAC … V tRNA
• The ribosome matches UAC on tRNA with AUG on mRNA, then uses the M on the other end in the protein.
![Page 34: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/34.jpg)
mRNA goes to a ribosome
• AUGGUGCAUCUGACUCCU… mRNA
• UAC …. M tRNA• CAC … V tRNA
• The ribosome matches CAC on tRNA with GUG on mRNA, then uses the V on the other end to extend the protein.
![Page 35: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/35.jpg)
Ribosome
• In this manner, the ribosome continues to make the protein until it reaches a STOP codon.
![Page 36: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/36.jpg)
When is a given gene being expressed?
• A given protein is being made when its mRNA is present in the cell.
• The DNA is always present.
![Page 37: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/37.jpg)
When is a given gene being expressed?
• To tell what is being expressed at a given time in a given cell, find out which mRNAs are present.
• For each kind of mRNA, measure the quantity present.
![Page 38: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/38.jpg)
A microarray
![Page 39: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/39.jpg)
Microarrays
• A microarray consists of a pattern of thousands of features.
• Each feature has some DNA that will probe and possibly bind with an mRNA sample.
• Typically the feature is made to fluoresce under the presence of binding mRNA.
• The brightness of the dot corresponds to the quantity of mRNA of the given sort that is present.
![Page 40: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/40.jpg)
Two gene chips
![Page 41: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/41.jpg)
Microarrays
• Typically the probe is attached to a solid surface which is a glass or silicon chip. It is then called a gene chip or Affymetrix microarray.
![Page 42: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/42.jpg)
Introns
• Introns are inserts in the DNA within portions that code for one protein.
• The parts that code are exons.
![Page 43: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/43.jpg)
Introns must be removed to make the mature mRNA
![Page 44: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/44.jpg)
cDNA
• Complementary DNA (cDNA) is DNA synthesized from mature mRNA using reverse transcriptase.
• AUGGUGCAUCUG mRNA• TACCACGTAGAC cDNA
![Page 45: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/45.jpg)
cDNA
• cDNA is more stable than RNA.
• cDNA corresponds with the part of the genome from which introns have been removed.
• cDNA does not correspond exactly to nuclear DNA.
![Page 46: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/46.jpg)
The mature mRNA
![Page 47: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/47.jpg)
The probes
• Each dot can contain DNA, cDNA, or an oligonucleotide (oligo).
• An oligonucleotide is a short fragment of single-stranded DNA, typically 5 to 50 nucleotides long.
![Page 48: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/48.jpg)
Gene expression profiling
• In an mRNA or gene expression profiling experiment the expression levels of thousands of genes are monitored simultaneously in parallel. This can be used to distinguish
• (a) the effects of certain treatments• (b) the effects of diseases• (c) the effects of different stages of
development.
![Page 49: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/49.jpg)
Gene expression profiling
• For example, microarrays can identify genes whose expression is changed in response to pathogens by comparing gene expression in infected cells to that in uninfected cells.
![Page 50: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/50.jpg)
A microarray experiment
• Suppose there are two cells--type 1, healthy, and type 2, diseased. Both have four genes A, B, C, D. We want to compare the expression of these genes in the two types of cell.
![Page 51: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/51.jpg)
Procedure
• 1. Prepare the DNA chip using the chosen target DNAs.
• 2. From the cells, isolate the mRNA.• 3. Use the mRNA as templates to generate
cDNA with a fluorescent tag attached. Typically a green fluorescent tag is used for mRNA from healthy cells, while a red tag is used for mRNA from diseased cells.
![Page 52: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/52.jpg)
Procedure
• 4. Prepare a hybridization solution with a mixture of the fluorescently labeled cDNAs.
• 5. Incubate the hybridization solution with the DNA chip.
• 6. Detect bound cDNA using laser technology.
• 7. Analyze the data.
![Page 53: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/53.jpg)
Appearance afterwards
![Page 54: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/54.jpg)
Interpreting colors
• A spot with just healthy cDNA is green.
• A spot with just diseased cDNA is red.
• A spot with both is yellow.
• A spot with neither is black.
![Page 55: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/55.jpg)
Comparison of cells
• Microarrays are used to compare the genome content in different cells for the same organism.
![Page 56: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/56.jpg)
Single Nucleotide Polymorphisms
• A single nucleotide polymorphism is a single substitution in the genome.
• Example:
• AUGGUGCAUCUGACUCCU standard
• AUGGUGUAUCUGACUCCU SNP
![Page 57: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/57.jpg)
Detecting SNPs
• Microarrays can be used to detect SNPs between or within populations.
• This can measure predisposition to diseases or identify appropriate drugs.
![Page 58: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/58.jpg)
How are chips made?
• In spotted microarrays the probes may be small fragments of DNA. An array of fine needles is controlled by a robotic arm that is dipped into wells containing the DNA probes. Each needle then deposits a probe at the desired location on the surface. The probes are fixed to the surface. Then the chip is ready to be washed in a solution containing the targets.
![Page 59: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/59.jpg)
DNA microarray being printed by a robot
![Page 60: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/60.jpg)
Flexibility of microarrays
• Thus scientists can produce arrays from their own labs, customized to an experiment.
![Page 61: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/61.jpg)
Bioinformatics problems
• 1. How long should the probes be (i.e., how many nucleotides long)?
• If too short, you get false signals.
• If too long, it is expensive.
![Page 62: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/62.jpg)
Bioinformatics problems
• 2. Which parts of a sequence should be cloned in the probe?
![Page 63: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/63.jpg)
DNA for beta hemoglobin
• ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAA
![Page 64: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/64.jpg)
Statistical issues in microarrays
• 1. There is variability in how well each probe in the microarray was made.
• 2. There is variability in how uniformly the target got washed across the chip.
• 3. There is variability in how accurately the probe binds with the target.
![Page 65: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/65.jpg)
Statistical questions
• What level of expression is statistically significant?
• If there are 20,000 probes, a 95% confidence means there are ? events with probability less than 5%.
![Page 66: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/66.jpg)
Statistical questions
• What level of expression is statistically significant?
• If there are 20,000 probes, a 95% confidence means there are 1000 events with probability less than 5%.
![Page 67: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/67.jpg)
Statistical issues
• How can the data be normalized (ie, compared with known probability distributions, like the normal curve)?
• P values: there will be false positives and false negatives.
![Page 68: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/68.jpg)
Experimental design issues
• Replication of biological samples
• Replication of RNA samples from each experiment
• Replicate each spot on the microarray
![Page 69: Gene Expression. Gene expression All cells in one organism have the same DNA. But different cells have very different functions. In each cell at certain](https://reader035.vdocuments.site/reader035/viewer/2022062805/5697c0081a28abf838cc6965/html5/thumbnails/69.jpg)
Data warehousing
• The data bases are huge hence hard to understand.